Vessels, Pumps and VIs – Oh My!

Since my last post I have completely re-designed my chemostat system. Take a look at my last blog post to see a picture of the previous system (aka Cv1.0). Although good in theory (autoclavable culture vessel, large culture volume, inexpensive to implement), many problems came out in the test culture phase.

To begin with, although the culture vessel itself was indeed autoclavable, the bulkhead fittings that connected tubing to the vessel were not. The silicone sealant used to close off gaps was also not autoclavable.

Additionally, the peristaltic pumps for this system quickly became very unreliable and refused to stay synchronized. Since the principle of a chemostat system is dependent on constant, synchronized influx and efflux of media, lack of synchronization in the input/output pumps leads to serious problems such as excessive dilution of the culture or (far worse) draining the culture vessel dry.

The culture vessel for Cv1.0 was also far too large. Topping out at 4 liters, it required an enormous amount of media to keep the culture at steady state.

Because of these problems I have decided to adopt a new system design (Cv2.0). Instead of the previous two pump chemostat system (one input pump and one output pump), the new system is an overflow chemostat. This simply means that the culture vessel has an open port in the side of the flask that drains excess media when the media level rises to the overflow level. This has the great benefit of requiring only one media pump (the input pump) since the overflow port drains media at the same rate that it is being pumped into the system. This new culture vessel is also much smaller (2L media capacity), so media demands should be less. Upgrading to a better quality peristaltic pump seems to have solved the flow inconsistency problems experienced in the previous system.

I have also begun the process of writing a LabVIEW VI (virtual instrument) to control the gas manifold (see picture) in response to culture pH. Slowly but surely, progress is being made.

Gas manifold with solenoid valves and non-compressible gas lines

In between working over my chemostat I have been writing my thesis proposal. It looks like I’ll be defending my proposal sometime in March or April, so I’ve also been working on some preliminary data to relate Alexandrium cellular health to pH. Hopefully I’ll be including this in my next post.

Happy 2013! :)



Greetings oceanophiles! As this is my first blog post as a Sea Grant scholar, I feel I should give a little background about myself. I am just beginning my second year as a Ph.D. student with Drs. Tawnya Peterson and Joseph Needoba at Oregon Health & Science University in Beaverton, OR. My degree track is Environmental Science and Engineering, with a focus on Estuary and Ocean Systems. I have always loved the Pacific Northwest, and am constantly amazed that I get to study it for a living.

So what am I actually doing? The goal of my research is to identify links between pH and pCO2 concentration in the water and population dynamics of harmful algal blooms (HABs) in the northern California Current system. My research specifically focuses on the marine dinoflagellate Alexandrium. This little guy is the alga that is primarily responsible for paralytic shellfish poisoning (PSP) events off the west coast of North America. Alexandrium produces saxitoxin, an extremely potent neurotoxin. Shellfish are filter feeders, and accumulate toxins when they feed on HAB species in the surrounding water. When there is an increased number of Alexandrium in the water (as frequently happens in the summer months), saxitoxin builds up to dangerous levels in the shellfish and can cause paralysis in humans and animals. What I want to do is discover whether there is a link between the pH/pCO2 content of the water and population dynamics and toxin production of Alexandrium.

I expect to be spending a lot of time on boats in the next few years, stalking the wild Alexandrium through the Columbia River estuary and out on the coast, but I will probably spend far more time in the lab. To that end, I am in the process of building a chemostat culture system, which will grow algae at a constant rate in a nutritionally static environment. Influx and efflux of media to and from the culture vessel are synchronized to the growth rate of the algae to maintain a constant growth rate.


The constant influx of fresh media and efflux of waste will ensure that the nutrient load of the culture vessel remains constant. I also designed the system to automatically monitor and control pH using a custom made pneumatic manifold that will change the pH of the culture vessel by bubbling it with CO2 gas. The monitoring will be accomplished by a Labview program that will also allow for remote monitoring of the system, and send will me alarms if/when something goes wrong. I have already finished the first iteration of the chemostat system and am in the process of working out the bugs (waste overflows, variable pump rates, etc.).

I’m excited to see where this year will take me and to see what new adventures lie in wait, both in the lab and out on the water. Tallyho!